Tue Nov 22 14:18:03 PST 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:18:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6502758 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 0.6502758 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1952 total number of charged atoms : 1820 net assigned charge : 3.000004 assigned positive charge : 291.4139 centred at (gu) : 90.06283 92.03792 89.84064 assigned negative charge : -288.4142 centred at (gu) : 89.97620 92.15696 89.91306 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5712 nv = 96 ne = 84 npr = 39385 no. pairs analyzed = 39385 no. exposed pairs = 2550 no. arc points = 17697 no. surface atoms = 867 nbur = 1085 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3106 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1755 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4772181E-08 -2.0892124E-09 midg,1,midg; midg,igrid,midg 1.2721337E-08 -1.2050404E-08 1,midg,midg; igrid,midg,midg -3.7599013E-09 1.6083305E-08 gauss-seidel spectral radius is 0.9876911 estimated iterations to convergence 74 setup time was (sec) 0.4300000 now iterating at: 14:18:11 rms-change max change #iterations 0.1377621 20.68145 at 10iterations 1.3889853E-02 2.111492 at 20iterations 1.4481579E-03 0.2299290 at 30iterations 1.4862070E-04 2.3056746E-02 at 40iterations 1.5053640E-05 2.3689270E-03 at 50iterations finished qdiffx linear iterations at : 14:18:18 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 1.5053640E-05 2.3689270E-03 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 14:18:20 3.029u 0.139s 0:12.67 24.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:18:22 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.950827 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 1.950827 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1952 total number of charged atoms : 1820 net assigned charge : 3.000004 assigned positive charge : 291.4139 centred at (gu) : 90.18827 96.11371 89.52187 assigned negative charge : -288.4142 centred at (gu) : 89.92886 96.47104 89.73936 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 61116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17697 grid for indexing accessible points = 1.400000 m= 22814 mr = 41716 m= 3827 mr = 17131 m= 245 mr = 2533 m= 3 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 745 time to turn everything in is 0.4400000 number of dielectric boundary points 26535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14378 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6502758 object centre at (A) : 12.33450 -19.40750 -27.07600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8330329E-03 4.7809172E-02 midg,1,midg; midg,igrid,midg 4.1320853E-02 -8.9937923E-03 1,midg,midg; igrid,midg,midg -3.7702753E-03 6.7821373E-03 gauss-seidel spectral radius is 0.9986254 estimated iterations to convergence 214 setup time was (sec) 0.7000000 now iterating at: 14:18:27 rms-change max change #iterations 3.802552 181.8695 at 10iterations 1.778221 69.50521 at 20iterations 0.8293054 30.99519 at 30iterations 0.3870682 15.46620 at 40iterations 0.1808275 5.906372 at 50iterations 8.4079638E-02 3.036958 at 60iterations 3.9273102E-02 1.301449 at 70iterations 1.8343141E-02 0.6340122 at 80iterations 8.5625770E-03 0.3285351 at 90iterations 3.9893682E-03 0.1349192 at 100iterations 1.8573325E-03 7.0157290E-02 at 110iterations 8.6892972E-04 2.9708862E-02 at 120iterations finished qdiffx linear iterations at : 14:18:46 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 8.6892972E-04 2.9708862E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 14:18:48 6.946u 0.156s 0:26.88 26.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:18:50 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.926241 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 2.926241 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1952 total number of charged atoms : 1820 net assigned charge : 3.000004 assigned positive charge : 291.4139 centred at (gu) : 90.28249 99.17055 89.28271 assigned negative charge : -288.4142 centred at (gu) : 89.89334 99.70663 89.60916 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 140999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17697 grid for indexing accessible points = 1.400000 m= 72602 mr = 100852 m= 27746 mr = 59756 m= 7067 mr = 22801 m= 1126 mr = 5515 m= 77 mr = 802 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 2510 time to turn everything in is 1.070000 number of dielectric boundary points 59848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 14560 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.950827 object centre at (A) : 12.33450 -19.40750 -27.07600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9142243E-02 0.8555722 midg,1,midg; midg,igrid,midg 0.4137429 -0.1669070 1,midg,midg; igrid,midg,midg -3.5321496E-02 3.3436213E-02 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 1.350000 now iterating at: 14:18:57 rms-change max change #iterations 8.880605 398.4599 at 10iterations 5.106384 120.8748 at 20iterations 2.923877 59.82443 at 30iterations 1.676113 35.38152 at 40iterations 0.9561986 19.10921 at 50iterations 0.5460587 11.95589 at 60iterations 0.3115367 6.416550 at 70iterations 0.1774456 3.908302 at 80iterations 0.1013639 1.924751 at 90iterations 5.7809252E-02 1.331785 at 100iterations 3.3013053E-02 0.6598415 at 110iterations 1.8865997E-02 0.3717079 at 120iterations 1.0724030E-02 0.2134399 at 130iterations 6.1249328E-03 0.1234550 at 140iterations 3.4915926E-03 6.9173813E-02 at 150iterations 1.9884661E-03 4.0681362E-02 at 160iterations 1.1381733E-03 2.1991730E-02 at 170iterations 6.4944651E-04 1.3545990E-02 at 180iterations finished qdiffx linear iterations at : 14:19:29 total time elapsed so far: 11.62000 # loops : 180 mean,max change (kT/e) : 6.4944651E-04 1.3545990E-02 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 14:19:31 11.790u 0.200s 0:41.53 28.8% 0+0k 0+0io 0pf+0w